PLEASE NOTE NEW VOLUME AND CONCENTRATION REQUIREMENTS
Samples can be submitted in PCR strip tubes or PCR plates for Sanger sequencing using the following process and guidelines. A maximum of 92 samples can be submitted in a 96-well plate to allow for the inclusion of controls. Your order request must be submitted online using dnaLIMS prior to physically submitting your samples:
Process
1
Prepare samples specific for the preferred service level, and follow the recommended protocol
2
Enter your order request online using dnaLIMS, and submit samples with a printed copy of your request form together in a sealed bag.
3
Drop off in-person, by campus mail, or by courier to:
Sequencing and Bioinformatics Consortium
University of British Columbia
Room 3124 - PharmSci Building
2405 Wesbrook Mall
Vancouver, BC V6T 1Z3
Submission deadines: 9:30 am for SBC_Core-Prepared samples or 1:00 pm for all other submissions
Samples can be left in the refrigerated dropbox on the main floor of the Pharmaceutical Sciences building (contact us for details).
Following these guidelines will ensure that your samples are processed without delay.
REMEMBER: Templates and primers should be resuspended in water or Tris (not TE), as EDTA will interfere with the ion concentration in the sequencing reaction.
A: SBC_Core-Prepared
- Template and primer are submitted separately.
- Template:
- We require a minimum of 10 µL of DNA sample at the concentration specified in the table below.
- DNA must be purified and quantified prior to submission. It is critical that the concentrations are measured carefully, as incorrect quantitation (whether higher or lower) will result in poor sequencing results. Please note that the required concentrations listed are based on UV absorbance / nanodrop and not fluorometric quantification. See also “How should I quantify my DNA prior to submission?” in our FAQ section: https://sequencing.ubc.ca/our-services-equipment/sanger-sequencing/sanger-faq
- If multiple reactions use the same template, please submit these as separate reactions (i.e. one 10 µl aliquot per reaction).
- For orders with fewer than 48 samples, submit your samples in 8-strip PCR tubes. ONLY label the side of the tubes with your initials and sample number. For orders with 48 or more samples, submit your samples in a 96-well PCR plate, filling in columns (e.g. A1 to H1). A maximum of 92 samples can be submitted in a 96-well plate to leave room for control samples. We can provide you with strips or plates if needed.
- Primer:
- If submitting custom primers, a minimum of 5 µL of primer at 5 pmol/µL is required per reaction.
- Primers should be submitted in 1.5 mL eppendorfs, with the primer name labelled on the lid with indelible ink.
- Templates and primers should be resuspended in water or Tris (not TE), as EDTA will interfere with the ion concentration in the sequencing reaction.
- Recommended concentrations are listed in the table below.
Standard Templates | Minimum Quantity Required (per reaction) | MInimum Quantity Required (per submission) | Concentration | Volume |
plasmid DNA | 200 ng | 400 ng | 40 - 250 ng/µL | >10 µLper reaction |
purified PCR product (100 - 300 bp) | 5 ng | 10 ng | 1 - 20 ng/µL | >10 µL per reaction |
purified PCR product (301 - 1,000 bp) | 15 ng | 30 ng | 3 - 40 ng/µL | >10 µL per reaction |
purified PCR product (over 1,000 bp) | 50 ng | 100 ng | 10 - 200 ng/µL | >10 µL per reaction |
Other Templates | ||||
cosmid/fosmid/BAC (over 20 kbp) | 600 ng | 1200 ng | 500 - 800 ng/µL | >10 µL per reaction |
Custom primer, if required* | ||||
primer, submitted separately from template | 5 pmol/µL | >5 µL per reaction | ||
*only required if a standard sequencing primer is not specified
Please read important information on template/primer considerations in our submission guidelines.
B: User-Prepared, Pre-Mixed
- Template and primer are submitted pre-mixed with water. Our staff add sequencing chemistry, perform cycling, post-reaction clean-up, and electrophoreses.
- We require 14 µL of sample, containing template and primer at the amounts specified in the table below, mixed with water as needed.
- It is critical that the concentrations are measured carefully, as incorrect quantitation (whether higher or lower) will result in poor sequencing results. Please note that the required concentrations listed are based on UV absorbance / nanodrop and not fluorometric quantification. See also “How should I quantify my DNA prior to submission?” in our FAQ section: https://sequencing.ubc.ca/our-services-equipment/sanger-sequencing/sanger-faq
Standard Template | Final Amount Required | Total volume |
Plasmid DNA | 400 ng | 14 µL |
purified PCR product (100 - 300 bp) | 10 ng | 14 µL |
purified PCR product (301 - 1,000 bp) | 30 ng | 14 µL |
purified PCR product (over 1,000 bp) | 100 ng | 14 µL |
primer | 10 pmol | included in above |
Other Templates | ||
cosmid/fosmid/BAC (over 20 kbp) | 1200 ng | 14 µL |
primer | 10 pmol | included in above |
- For orders with fewer than 48 samples, submit your samples in 8-strip PCR tubes. ONLY label the side of the tubes with your initials and sample number. For orders with 48 or more samples, submit your samples in a 96-well PCR plate, filling in columns (e.g. A1 to H1). We can provide you with strips or plates if needed. A maximum of 92 samples can be submitted in a 96-well plate to leave room for control samples
- Templates and primers should be resuspended in distilled water or 10 mM Tris pH 7-8, with no EDTA, as EDTA will interfere with the ion concentration in the sequencing reaction.
C: User-Prepared, SBC_Core-Cleaned
- User performs the cycle sequencing with ABI Big Dye 3.1 Cycle Sequencing kit, and submits cycled product for post-reaction cleaning, injection, and electrophoretic separation.
- We require 12 µL of cycled material.
- For orders with fewer than 48 samples, submit your samples in 8-strip PCR tubes. Label the side of the tubes with your initials and sample number. For orders with 48 or more samples, submit your samples in a 96-well PCR plate, filling in columns (e.g. A1 to H1). We can provide you with strips or plates if needed. A maximum of 92 samples can be submitted in a 96-well plate to leave room for control samples
- Templates and primers should be resuspended in distilled water or 10 mM Tris pH 7-8, with no EDTA, as EDTA will interfere with the ion concentration in the sequencing reaction.
D: User-Prepared, User-Cleaned
- User performs the cycle sequencing and post-reaction clean-up, and submits samples for injection and electrophoretic separation.
- We require 12 µL of sample resuspended in water, not formamide.
- For orders with fewer than 48 samples, submit your samples in 8-strip PCR tubes. Label the side of the tubes with your initials and sample number. For orders with 48 or more samples, submit your samples in a 96-well PCR plate, filling in columns (e.g. A1 to H1). We can provide you with strips or plates if needed.
- Templates and primers should be resuspended in distilled water or 10 mM Tris pH 7-8, with no EDTA, as EDTA will interfere with the ion concentration in the sequencing reaction.
Protocol: Standard Sequencing (Plasmid, PCR Product)
Reaction Set-up
Plasmid DNA
Template | 200 ng |
Primer | 5 pmol |
BigDye® dilution mix | 3 µL |
dH2O to final volume: | 10 µL |
PCR Product (choose product length)
Template (100-300bp) | 5 ng |
OR (301-1000bp) | 15 ng |
OR (over 1000bp) | 50 ng |
Primer | 5 pmol |
BigDye® dilution mix | 3 µL |
dH2O to final volume: | 10 µL |
BigDye® dilution mix can be purchased from SBC (please see services and pricing)
Cycling Protocol
(ramp rate = 1°C/sec)
hot start | 96°C | 1 min |
25x | 96°C | 10 sec |
50°C | 5 sec | |
60°C | 4 min | |
soak | 4°C | 8 |
.
Protocol: Specialty Sequencing (COSMID, BAC)
Reaction Set-up
Cosmid/BAC
Template | 600 ng |
Primer | 5 pmol |
BigDye® dilution mix | 3 µL |
dH2O to final volume: | 10 µL |
BigDye® dilution mix can be purchased from SBC (please see services and pricing)
Cycling Protocol
hot start | 96°C | 1 min |
50x | 96°C | 10 sec |
50°C | 5 sec | |
60°C | 4 min | |
soak | 4°C | 8 |
Template and Primer Requirements
Template Considerations
Of primary importance to the success of DNA sequencing reactions is the quality and quantity of sample provided. SBC cannot be held responsible for failures in sequencing which are related to poor preparation of the DNA template used, or failure to follow recommended guidelines.
- Contaminated template will give high background noise and poor, or no, sequence information
- Many of the commercially-available extraction and purification kits (eg. Qiagen, Promega, Wizard Plus, Sigma) are recommended
- *** Please ensure that the elution buffer does NOT contain EDTA ***
- It is critical that the concentrations are measured carefully, as incorrect quantitation (whether higher or lower) will result in poor sequencing results. Please note that the required concentrations listed are based on UV absorbance / nanodrop and not fluorometric quantification. See also “How should I quantify my DNA prior to submission?” in our FAQ section: https://sequencing.ubc.ca/our-services-equipment/sanger-sequencing/sanger-faq
- Modified conditions available for “difficult” templates (GC-rich, poly-T)
Primer Considerations
Recommendations when designing custom sequencing primers:
- Tm between 55°C and 60°C
- Formula: ºC = 4(G+C) + 2(A+T)
- “G” or “C” at 3’end
- avoid primers with runs of 3 or more of the same base
- use primer design software to avoid primers with hairpin or dimer characteristics
Custom primers must be submitted at a concentration of 5pmol/µl, resuspended in distilled water or 10 mM Tris pH 7-8, with no EDTA.
Standard Sequencing Primers available at SBC
Orientation Grid